Tag Archives: humor

What Was I Thinking?

The LTEE has run for over 10,000 days and almost 67,000 generations. It’s time to shut it down, as of today.

It’s been a hell of a lot of work, and we have almost nothing to show for it. As some astute commentators have noted around the web, the creatures in the flasks are still just bacteria—creatures, just as they were created.

If you read the first LTEE paper*, you’ll see we predicted the bacteria should become yeast by about 5,000 generations, nematodes at 15,000 generations or so, and fruit flies by 30,000 generations, maybe 35,000 at the outside.

After that, we’d have to stop the experiment anyhow, because we wouldn’t be able to freeze and bring them back alive any longer.

Plus, we’d have to get IRB approval for human experimentation if we ran it much past 50,000 generations.

Well, we’ve given the LTEE all this time, and still … they ’re just bacteria. I guess we’ve proven that Charles Darwin was wrong after all.

As an astute reviewer pointed out when we submitted that first paper, “I feel like a professor giving a poor grade to a good student.”  I should’ve listened and quit way back then. It would’ve saved everyone a lot of time and effort.

Now it’s going to be a hell of a lot of work next week emptying the freezers and autoclaving all those samples.

* Lenski, R. E., M. R. Rose, S. C. Simpson, and S. C. Tadler. 1991. Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. American Naturalist 138: 1315-1341.

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A Birthday Sonnet

This past weekend, I celebrated my 60th birthday with friends and family from all over. One of the roasters was Ben “The Bard” Kerr, a professor at the University of Washington and colleague in the BEACON Center for the Study of Evolution in Action.

Borrowing from another bard, Ben waxed poetic about one of the lineages in the long-term evolution experiment and raised a toast with this Shakespearean flask.

 

Ben Kerr's Skakespearean flask

ODE TO AN LTEE LINEAGE

Shall I compare Ara-3 to a summer’s day?

Thou start more humbly, but sure potentiate.

Rough spins do shake the darling bugs of Rich’s gaze,

And latecomer’s “fleece” hath all to port citrate.

One line’s long-shot passed by eleven lines,

And how was its controlled complex “skin” pinned?

Promoter capture, over some time refined.

By chance, with nature’s arranging force, trimmed.

But thy Cit-minus partner shall not fade

Nor gain possession of the flair of most

C4 shall Cit snag, now spawned by carbon trade

Then on it turns ‘til lines will species now boast

     So long these cells can achieve, so wise to see,

     So long lives this work- and awe is rife, Lenski.

 

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Another Birthday Haiku

As I said in my last post, I just celebrated my 60th birthday with lots of friends and family. Several folks produced new artistic works, including two lovely haikus that celebrate the E. coli long-term evolution experiment.

Here’s one from Mike Wiser, who did his doctoral research on the long-term lines. A highlight of his work was a paper showing that fitness trajectories in these populations tend to follow a power law, which has no upper bound, rather than an asymptotic rectangular, as I had previously assumed.

Living things adapt.
Evolution keeps going.
No peak yet in sight.

 

Power law prediction, 2013

[The power-law model (blue) predicts future fitness gains much more accurately than does the hyperbolic model (red).  Image modified from Wiser et al. (2013, Science 342: 1364-1367) and shown here under the doctrine of fair use.]

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Birthday Haiku

This past weekend I had my 60th birthday. I was delighted to celebrate it with wonderful colleagues, students, friends, and family.

At a dinner roast and toast, everyone sang When We’re Sixty Four (Thousand), a tribute from the E. coli in the LTEE to the People of the Lab. And several friends came up with new contributions at the intersection of science and culture.

This beauty is from Andy Ellington, a professor in the Center for Systems and Synthetic Biology at the University of Texas and a member of the BEACON Center. As background, Andy coauthored a recent paper that helps to elucidate how one LTEE population evolved the novel ability to use citrate.

Without further ado, here’s his haiku …

Citrate just beyond.

Acetate potentiates.

Glucose is all gone.

 

Citrate

[Image of citrate molecule from Wikimedia Commons]

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When We’re Sixty Four (Thousand)

From the E. coli in the LTEE to the People of the Lab

[To be sung along to this Beatles classic]

 

When we get older, losing our fimbriae,

Many years from now,

Will you still be sending us our thiamine,

Birthday greetings, Erlenmeyer wine?

If we were mutants, crazy and fit,

Would that make you snore?

Will you still feed us, will you still freeze us,

When we’re sixty-four?

 

You’ll be older too,

And if you say the word,

We’ll evolve with you.

 

We could be handy, helping your pubs,

When your grants are gone.

You can write a paper by the fireside,

Weekend days give no time to hide.

Colonies growing, dotting the plates,

Who could ask for more?

Will you still feed us, will you still freeze us,

When we’re sixty-four?

 

Every summer you can buy a freezer when the space gets tight,

If it’s not too dear.

Save our clonal mix,

Plus and minus progeny,

Ara One to Six.

 

Keeping the notebook, pipetting each drop,

Track trajectories.

Indicate precisely what you think will change.

Hypothesize, test, unlimited range.

Give us your data, sequence and store,

Evolving evermore.

Will you still feed us, will you still freeze us,

When we’re sixty-four?

 

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Bacterial Niche Finally Defined

The following scholarly contribution comes from my wife Madeleine Lenski after conversing with her “sister” (my former postdoc) Valeria Souza.

For those with an itch for criteria,

Scratch this: What’s a niche for bacteria?

Don’t take me to task

If I answer “a flask” –

It’s a bitch from warm broth to Siberia.

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January 19, 2016 · 9:08 pm

Erdös with a non-kosher side of Bacon

Erdös number

Paul Erdös was a prolific and important mathematician. He also had hundreds of collaborators from around the world who coauthored papers with him.

Years ago, Casper Goffman explained an idea, called the Erdös number, that describes the “collaborative distance” between Erdös and someone else, where that distance is defined by the smallest number of steps based on coauthored papers. Erdös himself has an Erdös number of 0, while the 511 mathematicians who wrote papers with Erdös have an Erdös number of 1. One of these people is Persi Diaconis, a professional magician and Stanford mathematician specializing in probability theory.

Over 9,000 people have Erdös numbers of 2, meaning they wrote a paper with one or more of Erdös’s coauthors but never wrote a paper with Erdös himself.  Two of these people are Berkeley professors Bernd Sturmfels, in the field of algebraic geometry, and Lior Pachter, a computational biologist.  (Sturmfels coauthored three papers with Diaconis, and he wrote other papers with two more people with Erdös numbers of 1.  Pachter wrote several papers with mathematician Daniel Kleitman, an Erdös coauthor.)

In 2007, I coauthored a paper with Pachter and Sturmfels in which we analyzed epistatic interactions to describe the geometric structure of a fitness landscape:

Beerenwinkel, N., L. Pachter, B. Sturmfels, S. F. Elena, and R. E. Lenski. 2007. Analysis of epistatic interactions and fitness landscapes using a new geometric approach. BMC Evolutionary Biology 7:60.

So that paper gives me an Erdös number of 3.

Bacon number

A group of students later came up with the idea of a Bacon number, a Hollywood version of the Erdös number that equals the smallest number of film links separating any other actor from Kevin Bacon. (Bacon had been previously described as the “center of the Hollywood universe” after a 1994 interview in which he said he worked with everybody in Hollywood or someone who’s worked with them, according to Wikipedia.)

So Kevin Bacon has a Bacon number of 0, while actors who have appeared in a film with him have Bacon numbers of 1. An actor who appeared in a film with any actors who appeared with Bacon, but not in a film with Bacon himself, have a Bacon number of 2.

Morgan Freeman has a Bacon number of 1 based on a 2013 documentary film called “Eastwood Directs: The Untold Story.” (You missed that one? Me, too.) Well, a couple of weeks ago, I appeared in an episode of the show “Through the Wormhole with Morgan Freeman.”

Erdös-Bacon number

Now there’s a really special number called the Erdös-Bacon number, which is the sum of a person’s Erdös and Bacon numbers. Not many people have an Erdös number, and not many have a Bacon number. And very few people have an Erdös-Bacon number because you have to have written a math or science paper and appeared in a film, and of course with known connections to Erdös and Bacon along both paths.

Cornell mathematics professor Steven Strogatz has an Erdös-Bacon number of just 4, having appeared in a TV documentary film with Kevin Bacon called “Connected: The Power of Six Degrees.” Of course, that film is about the very sort of mathematical links we’re talking about here!

So someone just suggested to me that I now have an Erdös-Bacon number of 5. If so, that would put me ahead of such luminaries as Carl Sagan and Richard Feynman! Awesome!!

The fine print

As I was looking into this exciting possibility, I discovered a website called “The Oracle of Bacon.” It seems to be the semi-official arbiter of Bacon numbers, and it says: “We do not consider links through television shows, made-for-tv movies, writers, producers, directors, etc.”

That documentary about Cliff Eastwood, with both Morgan Freeman and Kevin Bacon in it, apparently doesn’t qualify.  So Morgan Freeman’s Bacon number rises to 2 (via many different paths through his many major films).

Even worse, though, my Bacon number evaporates entirely, since my link to Kevin Bacon goes through my appearance on a television show with Morgan Freeman.

So there you have it. I have an officially non-kosher Erdös-Bacon number of 5.

I guess I can live with that.

But if Kevin Bacon, Morgan Freeman, or any of their Hollywood friends invites me to appear in a real film, I’ll probably accept!

~~~

Note:  It looks like Steven Strogatz’s Erdös-Bacon number of 4 is also compromised because his Bacon number is through a TV movie.  You need to use non-default settings for it to show up on The Oracle of Bacon website.  But maybe it’s less non-kosher, since it was a TV movie, not just a TV show.

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